Sample size calculation for phylogenetic case linkage.

Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a s...

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Autores principales:	Shirlee Wohl, John R Giles, Justin Lessler
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/53799399176e4d65a5ab29e486fde76d
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spelling	oai:doaj.org-article:53799399176e4d65a5ab29e486fde76d2021-12-02T19:57:24ZSample size calculation for phylogenetic case linkage.1553-734X1553-735810.1371/journal.pcbi.1009182https://doaj.org/article/53799399176e4d65a5ab29e486fde76d2021-07-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009182https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies.Shirlee WohlJohn R GilesJustin LesslerPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 7, p e1009182 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Shirlee Wohl John R Giles Justin Lessler Sample size calculation for phylogenetic case linkage.
description	Sample size calculations are an essential component of the design and evaluation of scientific studies. However, there is a lack of clear guidance for determining the sample size needed for phylogenetic studies, which are becoming an essential part of studying pathogen transmission. We introduce a statistical framework for determining the number of true infector-infectee transmission pairs identified by a phylogenetic study, given the size and population coverage of that study. We then show how characteristics of the criteria used to determine linkage and aspects of the study design can influence our ability to correctly identify transmission links, in sometimes counterintuitive ways. We test the overall approach using outbreak simulations and provide guidance for calculating the sensitivity and specificity of the linkage criteria, the key inputs to our approach. The framework is freely available as the R package phylosamp, and is broadly applicable to designing and evaluating a wide array of pathogen phylogenetic studies.
format	article
author	Shirlee Wohl John R Giles Justin Lessler
author_facet	Shirlee Wohl John R Giles Justin Lessler
author_sort	Shirlee Wohl
title	Sample size calculation for phylogenetic case linkage.
title_short	Sample size calculation for phylogenetic case linkage.
title_full	Sample size calculation for phylogenetic case linkage.
title_fullStr	Sample size calculation for phylogenetic case linkage.
title_full_unstemmed	Sample size calculation for phylogenetic case linkage.
title_sort	sample size calculation for phylogenetic case linkage.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/53799399176e4d65a5ab29e486fde76d
work_keys_str_mv	AT shirleewohl samplesizecalculationforphylogeneticcaselinkage AT johnrgiles samplesizecalculationforphylogeneticcaselinkage AT justinlessler samplesizecalculationforphylogeneticcaselinkage
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Sample size calculation for phylogenetic case linkage.

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